In 1989, he became the head coach and athletic director of Fred T. Foard High School, near his hometown and alma mater Maiden, North Carolina,[2] where the Tigers went 0–10.[5] "[Wilson] was dealt a very ugly hand. There was very little talent and probably less commitment." Considering the environment in which Wilson was raised, it's no surprise he grew frustrated quickly that so many players at Fred T. Foard didn't share his passion for football. [6]

Following one year coaching on the high school level, Wilson returned to college coaching for the Miami UniversityRedHawks in 1990, under head coach Randy Walker, and coached there as offensive line coach, quarterbacks coach and offensive coordinator until 1998.[3] When Walker moved to Northwestern University Wilson went with him, serving as the offensive coordinator, quarterbacks coach, and assistant head coach, from 1999 to 2001.[7]

After spending 19 seasons under the tutelage of his mentor Walker (four as a player at North Carolina, three as a graduate assistant there, nine as a coach at Miami, and three as a coach at Northwestern),[8][9] Wilson left his long-time mentor to become the running game coordinator and the offensive line coach at Oklahoma in 2002.[10][11] In December 2005, Wilson was named the offensive coordinator for the Sooners prior to the 2006 season, replacing Chuck Long who left to become the head coach at San Diego State. Oklahoma named James Patton to replace Wilson as offensive line coach, Patton served under Wilson at both Northwestern and Miami, and Wilson recommended Patton to Sooners' head coach Bob Stoops.[12][13] In 2008, Wilson won the Broyles Award, which is given to the top assistant in college football annually.[14] He was also named the "FootballScoop Offensive Coordinator of the Year".[15]

Indiana athletic director Fred Glass announced the dismissal of Bill Lynch and the rest of the coaching staff on November 28, 2010, following a third straight season with only one conference victory. Glass announced the hiring of Wilson on December 7, giving Wilson his first collegiate head coaching position. Just thirteen days later Wilson hired New Mexico defensive coordinator Doug Mallory and Nebraska linebackers coach Mike Ekeler (also LBs) as co-defensive coordinators. Mallory, the son of former Indiana head coach Bill Mallory, was Indiana's defensive backs coach from 1994–1996. Wilson also hired Rod Smith from Michigan and Kevin Johns from Northwestern to be co-offensive coordinators. Wilson took over a Hoosiers team that had finished 10th or 11th in the Big Ten in each of the previous three seasons and had not been to a bowl since losing to Oklahoma State in the 2007 Insight Bowl.

Under Wilson's first year, the Hoosiers had a 1–11 record. In his second year, Indiana improved to 4-8 on the year with Wilson's team exhibiting an explosive offense, going from 80th nationally in pass offense to 19th and leading the Big Ten with 311.2 yards per game, in spite of losing the starting quarterback Tre Roberson in the season's second game.[16][17]

In 2015, Indiana finished the regular season with a 6-6 record and showed a much more competitive level of play in the Big Ten. Indiana received an invitation to play in the Pinstripe Bowl, their first bowl game since 2007. After the season ended, Wilson signed a 6-year, $15.3 million contract extension that ran through 2021.[18] He parted ways with Indiana on December 1, 2016 amidst reports alleging that he mistreated players, including pressuring one to play despite a back injury.[19]

Ohio State announced January 10, 2017 that Wilson had been hired as the offensive coordinator and tight ends coach under head coach Urban Meyer.[20][21] His first game with the Buckeyes was an away game against Indiana, his previous team.